def save(self, **kw):
# save User, made active
user = super(SignUpForm, self).save(commit=False)
user.is_active = True
user.save()
tb_user = TBUser(user=user, affiliation=self.cleaned_data['affiliation'])
tb_user.save()
return tb_user
def create_tb_user(self):
assert hasattr(self, 'cleaned_data'), "Do not call this method on an invalid form."
# save User, made inactive
#
user = self.save(commit=False) # get object
#user.is_active = False # set to inactive, use for activation link scenario
user.save() # save
# save TBUser
#
tb_user = TBUser(user=user, affiliation=self.cleaned_data['affiliation'])
tb_user.save()
return tb_user
def setUp(self):
"""
Create initial objects for testing
"""
self.test_user = User(username='******',
password=get_random_string(length=32))
self.test_user.save()
self.tb_test_user = TBUser(user=self.test_user, affiliation='HU')
self.tb_test_user.save()
test_params = {u'status':\
PredictDatasetStatus.objects.get(pk=DATASET_STATUS_FILE_RETRIEVAL_COMPLETE),\
u'has_prediction': False,\
u'description': u'ok',\
u'file_type': u'vcf',\
u'title': u'vcf - embed',\
u'file_directory':\
u'/some-dir-to-add-files/test_setup/tb_uploaded_files/tbdata_00000013',\
u'fastq_type': u'',\
u'dropbox_url': \
u'https://www.dropbox.com/sh/p6ses8376312bes/AAA7TB4GhErfLLfE7WPco79ha?dl=0',\
u'user': self.tb_test_user}
self.dataset_vcf = PredictDataset(**test_params)
self.dataset_vcf.save()
test_params2 = test_params.copy()
test_params2['file_type'] = FILE_TYPE_FASTQ
test_params2['fastq_type'] = FASTQ_PAIR_ENDED
self.dataset_fastq = PredictDataset(**test_params2)
self.dataset_fastq.save()
script_dirname = join(dirname(realpath(__file__)), 'test_script_dir')
self.pipleline_scripts_info = PipelineScriptsDirectory(name='test dir',\
script_directory=script_dirname)
self.pipleline_scripts_info.save()
def setUp(self):
"""
Create initial objects for testing
"""
self.test_user = User(username='******', password=get_random_string(length=32))
self.test_user.save()
self.tb_test_user = TBUser(user=self.test_user, affiliation='HU')
self.tb_test_user.save()
test_params = {u'status':\
PredictDatasetStatus.objects.get(pk=DATASET_STATUS_FILE_RETRIEVAL_COMPLETE),\
u'has_prediction': False,\
u'description': u'ok',\
u'file_type': u'vcf',\
u'title': u'vcf - embed',\
u'file_directory':\
u'/some-dir-to-add-files/test_setup/tb_uploaded_files/tbdata_00000013',\
u'fastq_type': u'',\
u'dropbox_url': \
u'https://www.dropbox.com/sh/p6ses8376312bes/AAA7TB4GhErfLLfE7WPco79ha?dl=0',\
u'user': self.tb_test_user}
self.dataset_vcf = PredictDataset(**test_params)
self.dataset_vcf.save()
test_params2 = test_params.copy()
test_params2['file_type'] = FILE_TYPE_FASTQ
test_params2['fastq_type'] = FASTQ_PAIR_ENDED
self.dataset_fastq = PredictDataset(**test_params2)
self.dataset_fastq.save()
script_dirname = join(dirname(realpath(__file__)), 'test_script_dir')
self.pipleline_scripts_info = PipelineScriptsDirectory(name='test dir',\
script_directory=script_dirname)
self.pipleline_scripts_info.save()
class PredictBasicTest(TestCase):
"""
Run basic tests with the PredictDataset object
"""
fixtures = ['initial_data']
def setUp(self):
"""
Create initial objects for testing
"""
self.test_user = User(username='******',
password=get_random_string(length=32))
self.test_user.save()
self.tb_test_user = TBUser(user=self.test_user, affiliation='HU')
self.tb_test_user.save()
test_params = {u'status':\
PredictDatasetStatus.objects.get(pk=DATASET_STATUS_FILE_RETRIEVAL_COMPLETE),\
u'has_prediction': False,\
u'description': u'ok',\
u'file_type': u'vcf',\
u'title': u'vcf - embed',\
u'file_directory':\
u'/some-dir-to-add-files/test_setup/tb_uploaded_files/tbdata_00000013',\
u'fastq_type': u'',\
u'dropbox_url': \
u'https://www.dropbox.com/sh/p6ses8376312bes/AAA7TB4GhErfLLfE7WPco79ha?dl=0',\
u'user': self.tb_test_user}
self.dataset_vcf = PredictDataset(**test_params)
self.dataset_vcf.save()
test_params2 = test_params.copy()
test_params2['file_type'] = FILE_TYPE_FASTQ
test_params2['fastq_type'] = FASTQ_PAIR_ENDED
self.dataset_fastq = PredictDataset(**test_params2)
self.dataset_fastq.save()
script_dirname = join(dirname(realpath(__file__)), 'test_script_dir')
self.pipleline_scripts_info = PipelineScriptsDirectory(name='test dir',\
script_directory=script_dirname)
self.pipleline_scripts_info.save()
def tearDown(self):
"""
Delete test objects
"""
self.dataset_vcf.delete()
self.dataset_fastq.delete()
self.tb_test_user.delete()
self.test_user.delete()
self.pipleline_scripts_info.delete()
def test_params_form(self):
# -------------------
# VCF file test
# -------------------
self.assertTrue(self.dataset_vcf.is_vcf_file(), "Should be a VCF file")
self.assertTrue(not self.dataset_vcf.is_fastq_file(),
"Should not be FastQ file")
self.assertEqual(self.dataset_vcf.get_file_patterns(),\
GENTB_VCF_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_vcf)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(
script_directory)
print script_command
self.assertTrue(script_command is not None)
#if script_command is not NOne:
# pipeline_runner.step3_run_command(script_command)
# -------------------
# FastQ file test
# -------------------
self.assertTrue(not self.dataset_fastq.is_vcf_file(),
"Should NOT be a VCF file")
self.assertTrue(self.dataset_fastq.is_fastq_file(),
"Should be a FastQ file")
self.assertEqual(self.dataset_fastq.get_file_patterns(),\
GENTB_FASTQ_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_fastq)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(
script_directory)
print script_command
self.assertTrue(script_command is not None)
class PredictBasicTest(TestCase):
"""
Run basic tests with the PredictDataset object
"""
fixtures = ['initial_data']
def setUp(self):
"""
Create initial objects for testing
"""
self.test_user = User(username='******', password=get_random_string(length=32))
self.test_user.save()
self.tb_test_user = TBUser(user=self.test_user, affiliation='HU')
self.tb_test_user.save()
test_params = {u'status':\
PredictDatasetStatus.objects.get(pk=DATASET_STATUS_FILE_RETRIEVAL_COMPLETE),\
u'has_prediction': False,\
u'description': u'ok',\
u'file_type': u'vcf',\
u'title': u'vcf - embed',\
u'file_directory':\
u'/some-dir-to-add-files/test_setup/tb_uploaded_files/tbdata_00000013',\
u'fastq_type': u'',\
u'dropbox_url': \
u'https://www.dropbox.com/sh/p6ses8376312bes/AAA7TB4GhErfLLfE7WPco79ha?dl=0',\
u'user': self.tb_test_user}
self.dataset_vcf = PredictDataset(**test_params)
self.dataset_vcf.save()
test_params2 = test_params.copy()
test_params2['file_type'] = FILE_TYPE_FASTQ
test_params2['fastq_type'] = FASTQ_PAIR_ENDED
self.dataset_fastq = PredictDataset(**test_params2)
self.dataset_fastq.save()
script_dirname = join(dirname(realpath(__file__)), 'test_script_dir')
self.pipleline_scripts_info = PipelineScriptsDirectory(name='test dir',\
script_directory=script_dirname)
self.pipleline_scripts_info.save()
def tearDown(self):
"""
Delete test objects
"""
self.dataset_vcf.delete()
self.dataset_fastq.delete()
self.tb_test_user.delete()
self.test_user.delete()
self.pipleline_scripts_info.delete()
def test_params_form(self):
# -------------------
# VCF file test
# -------------------
self.assertTrue(self.dataset_vcf.is_vcf_file(),
"Should be a VCF file")
self.assertTrue(not self.dataset_vcf.is_fastq_file(),
"Should not be FastQ file")
self.assertEqual(self.dataset_vcf.get_file_patterns(),\
GENTB_VCF_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_vcf)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(script_directory)
print script_command
self.assertTrue(script_command is not None)
#if script_command is not NOne:
# pipeline_runner.step3_run_command(script_command)
# -------------------
# FastQ file test
# -------------------
self.assertTrue(not self.dataset_fastq.is_vcf_file(),
"Should NOT be a VCF file")
self.assertTrue(self.dataset_fastq.is_fastq_file(),
"Should be a FastQ file")
self.assertEqual(self.dataset_fastq.get_file_patterns(),\
GENTB_FASTQ_FILE_PATTERNS)
pipeline_runner = PipelineScriptRunner(self.dataset_fastq)
script_directory = pipeline_runner.step1_get_script_directory_info()
self.assertTrue(script_directory is not None)
script_command = pipeline_runner.step2_get_script_command(script_directory)
print script_command
self.assertTrue(script_command is not None)
